Well day 2 of experimentation was a complete success. Again took her out on a long ride - stop and go - on the freeway, lots of stop and go - no dying. I don't want to get too excited but I am cautiously optomistic that I have indeed resolved the problem.
Those are really good ideas about securing the block-off caps with clamps or rubber bands. Cheap insurance.
And now that the smog stuff is all unhooked I think i'm going to stip it off completely and have a much cleaner look. You know, this whole thing was a good experience because it gave me a chance to really open her up and realize that she's not all that complex of a machine - something beautiful about the simplicity... and I love working on a bike with no f'ing fairings.
